But why? Won't that just make it far more awkward when they're inevitably forced to go through with very similar changes in the end?

Because now they can say "we considered it, there was strong opposition, and we didn't change the rules and what happened happened".

And if they miss out on part of a runup, and the companies later enter the index, what is the long term "harm" if any??

But if they're "right" it makes the competing indices look weak.